2 <head><title>Hidden Regions</title></head>
4 <p><strong>Hidden Regions</strong> </p>
5 <p>Use the keyboard key "H" to hide / reveal selected columns and sequences.
6 To hide / reveal only selected sequences, use "Shift H", to hide /
7 reveal only selected columns, use "Control H".</p>
8 <p><strong><em>Hiding Sequences</em></strong><br>
9 To hide selected sequences in an alignment, use the <strong>"View
10 -> Hide -> Selected Sequences"</strong> menu item or simply select <strong>"Hide
11 Sequences"</strong> from the Popup menu after a right click on the sequence Ids.
13 <p>Hidden sequences will not be used in any calculations, editing or web service
14 alignments performed on visible sequences. </p>
15 <p><strong><em>Hidden Sequences Representatives</em></strong><br>
16 A more advanced hide involves a right-mouse click on a sequence, then selecting
17 <strong>"SequenceID -> Represent Group with SequenceId"</strong>. Using this method
18 of hiding sequences, any edits performed on the visible group representative
19 will be propogated to all the sequences in that group. <br>
20 The hidden representative sequences will not be used in any
21 calculations or web service alignments (<em>nb. this may change in
24 <p><strong><em>Hiding Columns</em></strong><br>
25 To hide selected columns in an alignment, use the <strong>"View
26 -> Hide -> Selected Columns"</strong> menu item, or right click within a region
27 of selected columns in the scale above the alignment (only available in non
28 wrapped mode) and select <strong>"Hide Columns"</strong>. </p>
29 <p>When an alignment view contains hidden columns, certain constraints
30 apply:<ul><li>Editing the alignment is bound by the hidden columns, <em>i.e.</em> you cannot move residues
31 across a hidden column boundary.</li>
32 <li><strong>Tree</strong>, <strong>pairwise alignment</strong> and <strong>PCA</strong> calculations will only be
33 performed using the <em>visible</em> parts of the alignment.
36 href="../webservices/msaclient.html">Multiple Sequence
37 Alignments</a> are performed locally on on each visible chunk of
38 the input, and concatenated with the hidden regions to form the
42 <p><strong>Column Separability</strong><br>Calculations where hidden columns are
43 excluded, and a single analysis performed on the result, are termed <em>column-separable</em>.
44 The simple Tree and PCA calculations are column separable because essentially the same results
45 would be obtained if the excluded hidden columns were replaced by gaps as the input to the calculation.</p>
46 <p>Multiple Sequence alignment and secondary structure prediction are both non-column-separable, and
47 so the exclusion of hidden regions leads to only 'locally optimal' results - sometimes
48 different to that obtained when using the full alignment.</p>